Search Results (112)

This study describes the first complete genomic sequence of an NDM-19 and QnrS11-producing multidrug-resistant (MDR) Escherichia coli isolate collected from a fecal swab from a poultry farm in 2019 in Egypt. The bla_NDM-19 was identified by PCR screening and DNA sequencing. The isolate was then subjected to antimicrobial susceptibility testing, conjugation and transformation experiments, and complete genome sequencing. The chromosome of strain M2-13-1 measures 4,738,278 bp and encodes 4557 predicted genes, with an average G + C content of 50.8%. M2-13-1 is classified under ST167, serotype O101:H5, phylogroup A, and shows an MDR phenotype, having minimum inhibitory concentrations (MICs) of 64 mg/L for both meropenem and doripenem. The genes bla_NDM-19 and qnrS11 are present on 49,816 bp IncX3 and 113,285 bp IncFII: IncFIB plasmids, respectively. M2-13-1 harbors genes that impart resistance to sulfonamides (sul1), trimethoprim (dfrA14), β-lactams (bla_TEM-1B), aminoglycosides (aph(6)-Id, aph(3′)-Ia, aph(3″)-Ib, aac(3)-IV, and aph(4)-Ia), tetracycline (tet(A)), and chloramphenicol (floR). It was susceptible to aztreonam, colistin, fosfomycin, and tigecycline. The genetic context surrounding bla_NDM-19 includes ISAba125-IS5-bla_NDM-19-ble_MBL-trpF-hp1-hp2-IS26. Hierarchical clustering of the core genome MLST (HierCC) indicated M2-13-1 clusters with global ST167 E. coli lineages, showing HC levels of 100 (HC100) core genome allelic differences. Plasmids of the IncX3 group and the insertion sequence (ISAba125) are critical vehicles for the dissemination of bla_NDM and its related variants. To our knowledge, this is the first genomic report of a bla_NDM-19/IncX3-carrying E. coli isolate of animal origin globally. Full article

Escherichia coli (E. coli) is an opportunistic pathogen widely distributed in nature, and multi-drug resistance (MDR) E. coli has been widely recognized as a critical reservoir of resistance genes, posing severe health threats to humans and animals. A total of 288 E. coli strains were isolated and purified from fresh fecal samples of forest musk deer collected from farms in Sichuan, Shaanxi, and Yunnan Provinces of China between 2013 and 2023. This study aimed to conduct antibiotic susceptibility testing and resistance gene detection on the isolated forest musk deer-derived E. coli, analyze the correlations between them, investigate the presence of CRISPR systems within the strains, and perform bioinformatics analysis on the CRISPR systems carried by the strains. Results showed that 138 out of 288 E. coli strains were MDR, with the highest resistance to tetracycline (48.3%), cefalexin (45.1%), and doxycycline (41.7%). Prevalent genes were tetA (41.0%), sul2 (30.2%), blaTEM (27.1%), with 29 gene–phenotype pairs correlated. CRISPR system-negative strains had higher resistance rates to 16 antibiotics and lower detection rates only for aac (6′)-Ib-cr, qnrA, and qnrB compared to CRISPR system-positive strains. Regional analysis showed that the problem of drug resistance in Sichuan and Shaanxi was more serious, and that the detection rate of antibiotic resistance genes was relatively high. This study guides E. coli infection control in forest musk deer and enriches resistance research data. Full article

Ceftiofur sodium (CFS) is a clinically significant cephalosporin widely used in the livestock and poultry industries. However, CFS that is not absorbed by animals is excreted in feces, entering the environment and contributing to the emergence of antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs). This situation poses substantial challenges to both environmental integrity and public health. Currently, research on the biodegradation of CFS is limited. In this study, we isolated a strain of Escherichia coli, designated E. coli CS-1, a Gram-negative, rod-shaped bacterium capable of utilizing CFS as its sole carbon source, from fecal samples collected from hog farms. We investigated the effects of initial CFS concentration, pH, temperature, and inoculum size on the degradation of CFS by E. coli CS-1 through a series of single-factor experiments conducted under aerobic conditions. The results indicated that E. coli CS-1 achieved the highest CFS degradation rate under the following optimal conditions: an initial CFS concentration of 50 mg/L, a pH of 7.0, a temperature of 37 °C, and an inoculum size of 6% (volume fraction). Under these conditions, E. coli CS-1 was able to completely degrade CFS within 60 h. Additionally, E. coli CS-1 exhibited significant capabilities for CFS degradation. In this study, six major degradation products of (CFS) were identified by UPLC–MS/MS: desfuroyl ceftiofur, 5-hydroxymethyl-2-furaldehyde, 7-aminodesacetoxycephalosporanic acid, 5-hydroxy-2-furoic acid, 2-furoic acid, and CEF-aldehyde. Based on these findings, two degradation pathways are proposed. Pathway I: CFS is hydrolyzed to break the sulfur–carbon (S–C) bond, generating two products. These products undergo subsequent hydrolysis and redox reactions for gradual transformation. Pathway II: The β-lactam bond of CFS is enzymatically cleaved, forming CEF-aldehyde as the primary degradation product, which is consistent with the biodegradation mechanism of most β-lactam antibiotics via β-lactam ring cleavage. Transcriptome sequencing revealed that 758 genes essential for degradation were upregulated in response to the hydrolysis and redox processes associated with CFS. Furthermore, the differentially expressed genes (DEGs) of E. coli CS-1 were functionally annotated using a combination of genomics and bioinformatics approaches. This study highlights the potential of E. coli CS-1 to degrade CFS in the environment and proposes hypotheses regarding the possible biodegradation mechanisms of CFS for future research. Full article

Background/Objectives: The widespread use of antibiotics in animal husbandry has led to an increase in antimicrobial-resistant Escherichia coli, particularly strains producing extended-spectrum β-lactamases (ESBL) and AmpC β-lactamases. This study aimed to isolate and characterize such strains from fecal samples of broiler chickens (n = 71) and slaughtered turkeys (n = 31) in northwestern Romania. Methods: Antimicrobial susceptibility testing and PCR were used to evaluate phenotypic resistance patterns and detect the presence of resistance genes (AmpC, blaZ, and blaTEM). Results: The results showed that 55% of turkey and 61% of broiler isolates were presumptive ESBL/AmpC producers. Among all isolates, 50% were classified as extensively drug-resistant (XDR), 44% as multidrug-resistant (MDR), and only 6% were fully susceptible. Gene detection revealed an overall prevalence of 44.2% for AmpC, 72.7% for blaZ, and 58.1% for blaTEM, yielding a total penetrance of 51.09%. The diagnostic odds ratio (DOR) values, ranging from 0.67 to 81, suggest the efficacy of the antibiotic susceptibility testing method used in detecting the presence of these resistance genes. Conclusion: Overall, these findings highlight a significant burden of antimicrobial-resistant, poultry-associated E. coli strains, warranting stricter antimicrobial stewardship. Full article

Background/Objective. Toxin-producing strains of Clostridioides difficile (C. diff) are the most commonly identified cause of healthcare-associated infection in the elderly. Risk factors include advanced age, hospitalization, prior or concomitant systemic antibacterial therapy, chemotherapy, and gastrointestinal surgery. Patients with unspecified and new-onset diarrhea with ≥3 unformed stools in 24 h are the target population for C. diff infection (CDI) testing. To present data on the risks of laboratory misdiagnosis in managing CDI. Materials. In two general hospitals, we examined 116 clinical stool specimens from hospitalized patients with acute diarrhea suspected of nosocomial or antibiotic-associated diarrhea (AAD) due to C. diff. Enzyme immunoassay (EIA) tests for the detection of C. diff toxins A (cdtA) and B (cdtB) in stool, automated CLIA assay for the detection of C. diff GDH antigen and qualitative determination of cdtA and B in human feces and anaerobic stool culture were applied for CDI laboratory diagnosis. MALDI-TOF (Bruker) was used to identify the presumptive anaerobic bacterial colonies. The following methods were used as confirmatory diagnostics: the LAMP method for the detection of Salmonella spp. and simultaneous detection of C. jejuni and C. coli, an E. coli Typing RT-PCR detection kit (ETEC, EHEC, STEC, EPEC, and EIEC), API 20E and aerobic stool culture methods. Results. A total of 40 toxigenic strains of C. diff were isolated from all 116 tested diarrheal stool samples, of which 38/40 produced toxin B and 2/40 strains were positive for both cdtA and cdtB. Of the stool samples positive for cdtA (6/50) and/or cdtB (44/50) by EIA, 33 were negative for C. diff culture but positive for the following diarrheal agents: Salmonella enterica subsp. arizonae (1/33, LAMP, culture, API 20E); C. jejuni (2/33, LAMP, culture, MALDI TOF); ETEC O142 (1/33), STEC O145 and O138 (2/33, E. coli RT-PCR detection kit, culture); C. perfringens (2/33, anaerobic culture, MALDI TOF); hypermycotic enterotoxigenic K. pneumonia (2/33) and enterotoxigenic P. mirabilis (2/33, culture; PCR encoding LT-toxin). Two of the sixty-six cdtB-positive samples (2/66) showed a similar misdiagnosis when analyzed using the CLIA method. However, the PCR analysis showed that they were cdtB-negative. In contrast, the LAMP method identified a positive result for C. jejuni in one sample, and another was STEC positive (stx1+/stx2+) by RT-PCR. We found an additional discrepancy in the CDI test results: EPEC O86 (RT-PCR eae+) was isolated from a fecal sample positive for GHA enzyme (CLIA) and negative for cdtA and cdtB (CLIA and PCR). However, the culture of C. diff was negative. These findings support the hypothesis that certain human bacterial pathogens that produce enterotoxins other than C. diff, as well as intestinal commensal microorganisms, including Klebsiella sp. and Proteus sp., contribute to false-positive EIA card tests for C. diff toxins A and B, which are the most widely used laboratory tests for CDI. Conclusions. CDI presents a significant challenge to clinical practice in terms of laboratory diagnostic management. It is recommended that toxin-only EIA tests should not be used as the sole diagnostic tool for CDI but should be limited to detecting toxins A and B. Accurate diagnosis of CDI requires a combination of laboratory diagnostic methods on which proper infection management depends. Full article

The present study was conducted to assess the efficacy of Laboratory-Isolated Lactocaseibacillus casei NK1 (Lc. NK1) in broilers hypothesizing that, Lc. NK1 supplementation will enhance growth performance, modulate the gut microbiome, and reduce fecal pathogenic Escherichia coli in broilers. The experiment spanned 35 days where 60 one-day-old broiler chicks were randomly assigned to four treatment groups (n = 15); control-group with no treatment (NC), APEC (challenged with E. coli only), CProb (received commercial probiotics), and LNK1 (treated with Lc. NK1). The APEC, CProb, and LNK1 groups were infected with E. coli O78 strain at 11 days of age. Growth performance analysis revealed that the LNK1 group by day 35 gained body weight similar to the CProb group, with both groups significantly outperforming the APEC group (p < 0.001). Both the LNK1 and CProp groups exhibited similar reduction in E. coli while increasing Lactobacillus colorizations in the cloacal swabs from day 21 to 35 of age (p > 0.05). Metagenomic analysis using 16S rRNA sequencing showed that the LNK1 group maintained a diverse and balanced gut microbiota, characterized by increased Firmicutes and reduced Proteobacteria. In contrast, the APEC group exhibited reduced diversity and dominance of Escherichia-Shigella (p < 0.001). These findings suggest Lc. NK1 could be a promising probiotic for enhancing gut health and growth performance in broilers, even under pathogenic challenges, offering a potential alternative to antibiotics in poultry production. Full article

Antimicrobial resistance is increasingly becoming a serious public health issue. There is scientific evidence linking the use of antibiotics in livestock production to the emergence and spread of resistance in bacteria that are important for human health. To assess the prevalence of antimicrobial resistance in Escherichia coli and Enterococcus spp., fecal and slurry wastewater samples were collected from various cattle and swine farms, mainly located in the northern and central regions of Portugal. Samples from each farm were pooled for microbiological processing to isolate Escherichia coli and Enterococcus spp., followed by specific antibiotic susceptibility testing for each species using the disk diffusion method. The results of these analyses indicated a significant issue with tetracycline resistance in E. coli and Enterococcus spp. Furthermore, a notably higher frequency in resistant strains was observed in the majority of slurry samples compared to those derived from swine feces. This observation led to the hypothesis that slurry may provide a comprehensive historical perspective for studying the antibiotic resistance patterns present on a farm. Full article

Food safety, particularly within the meat industry, is a significant concern addressed under the One Health concept, emphasizing the necessity of enhanced surveillance and hygiene protocols to mitigate contamination risks. This study assessed microbiological risks in Romanian bovine slaughterhouses by analyzing 150 samples from stool and carcasses at the post-evisceration and cooling stages over seven months in two abattoirs, using standardized microbiological methods and PCR to quantify aerobic colony counts (ACCs), Enterobacteriaceae, and pathogens (E. coli, Salmonella spp., and Listeria spp.). ACCs and Enterobacteriaceae levels decreased significantly [p < 0.05] during processing, highlighting effective hygiene measures. Pathogenic E. coli was identified in 14% of fecal samples and 5% of carcasses, indicating cross-contamination risks. Salmonella spp. were found in 28% of fecal samples but absent on carcasses, suggesting successful containment. Listeria spp. were rare and not detected on carcasses. PCR confirmed the presence of pathogenic strains in stool samples, emphasizing the need for strict hygiene practices and regular monitoring to improve meat safety and protect public health. In conclusion, the prevalence of E. coli, particularly serogroups like O101 and O26, and the absence of Salmonella and Listeria in carcass samples reflect both regional differences in pathogenic strains and the need for comprehensive, multi-stage control measures. Further studies should broaden pathogen surveillance to include more E. coli serogroups and implement stricter hygiene protocols to prevent cross-contamination during evisceration, skinning, and cooling. Regular monitoring of Salmonella and Listeria, especially in silage-fed cattle regions, along with improved coordination across the food production, health, and environmental sectors, is essential to mitigate contamination risks and safeguard public health. Full article

To investigate the anti-bacterial and anti-inflammatory properties of sophoridine and elucidate its mechanism of action, we carried out both in vitro and in vivo experiments. Multiple bacterial strains were utilized to determine the effective concentration of sophoridine in antibacterial and bactericidal assays. Subsequently, LPS-stimulated RAW264.7 cells and E. coli-challenged BALB/c mice models were employed to evaluate the production of inflammatory cytokines. Our results showed that sophoridine concentrations exceeding 5.12 mg/mL significantly inhibited cell viability, while 0.32 mg/mL of sophoridine demonstrated the optimal anti-inflammatory activity at 12 h. In E. coli-induced diarrheal mice, doses of 15, 30, and 60 mg/kg BW of sophoridine alleviated fecal occult blood and exhibited anti-inflammatory effects by reducing the level of serum TNF-α, IL-1β, and IL-6 levels, increasing serum IL-10, and inhibiting leucocyte infiltration in the duodenum. Notably, 15 mg/kg BW of sophoridine effectively decreased the mRNA and protein expression of NF-κB p65. These findings suggest that sophoridine has promising potential for the treatment of diarrhea through its anti-inflammatory effects mediated by the inhibition of NF-κB activation. Full article

Iron uptake plays an important role in the persistence of Escherichia coli in the host and for its survival in the environment, and it is known that E. coli has a variety of siderophore systems for iron uptake. We investigated the ability to produce siderophores, the genetic diversity of the siderophores and their correlation with virulence-associated genes (VAGs), phylogroups and bacteriocin production in E. coli strains isolated from different sources: uropathogenic E. coli (UPEC) from urine of patients with urinary tract infections, avian pathogenic E. coli (APEC) from organs of birds with signs of colibacillosis, fecal E. coli (FEC) from feces of healthy cattle and E. coli from organic fertilizers based on poultry and cattle manure (OFEC). A high variability in siderophore production was found among the UPEC strains studied, while the OFEC strains showed the highest siderophore production among all groups. Genes for aerobactin and yersiniabactin receptors were most frequently found in the UPEC strain, followed by the APEC, FEC and OFEC strains. The greatest diversity of siderophore receptors was found in the APEC strain. We also found that iutA-positive E. coli isolated from animals contained more VAGs than iutA-negative strains. The profiles of the siderophore genes of APEC and OFEC from poultry manure were very similar, indicating that APEC can be transmitted via organic fertilizers, suggesting that poultry manure is an environmental risk. The data obtained complement the information on the prevalence of siderophore producers and contribute to our knowledge on the biodiversity of E. coli pathotypes. Full article

Background. Antibiotic-resistant (AR) bacteria pose an increasing threat to public health, but the dynamics of antibiotic resistance gene (ARG) spread in complex microbial communities are poorly understood. Conjugation is a predominant direct cell-to-cell mechanism for the horizontal gene transfer (HGT) of ARGs. We hypothesized that commensal Escherichia coli donor strains would mediate the conjugative transfer of ARGs to phylogenetically distinct bacteria without antibiotic selection pressure in gastrointestinal tracts of mice carrying a human-derived microbiota with undetectable levels of E. coli. Our objective was to identify a mouse model to study the factors regulating AR transfer by conjugation in the gut. Methods. Two donor E. coli strains were engineered to carry chromosomally encoded red fluorescent protein, and an ARG- and green fluorescent protein (GFP)-encoding broad host range RP4 conjugative plasmid. Mice were orally gavaged with two donor strains (1) E. coli MG1655 or (2) human-derived mouse-adapted E. coli LM715-1 and their colonization assessed by culture over time. Fluorescence-activated cell sorting (FACS) and 16S rDNA sequencing were performed to trace plasmid spread to the microbiota. Results. E. coli LM715-1 colonized mice for ten days, while E. coli MG1655 was not recovered after 72 h. Bacterial cells from fecal samples on days 1 and 3 post inoculation were sorted by FACS. Samples from mice given donor E. coli LM715-1 showed an increase in cells expressing green but not red fluorescence compared to pre-inoculation samples. 16S rRNA gene sequencing analysis of FACS GFP positive cells showed that bacterial families Lachnospiraceae, Clostridiaceae, Pseudomonadaceae, Rhodanobacteraceae, Erysipelotrichaceae, Oscillospiraceae, and Butyricicoccaceae were the primary recipients of the RP4 plasmid. Conclusions. Results show this ARG-bearing conjugative RP4 plasmid spread to diverse human gut bacterial taxa within a live animal where they persisted. These fluorescent marker strategies and human-derived microbiota transplanted mice provided a tractable model for investigating the dynamic spread of ARGs within gut microbiota and could be applied rigorously to varied microbiotas to understand conditions facilitating their spread. Full article

This study investigated the effects of a phytogenic feed additive (PFA) containing a blend of herbs, plant extracts and essential oils from the Lamiaceae, Schisandraceae, Zingiberaceae and Fabaceae families on the fecal score, intestinal histomorphology and fecal excretion of F4-fimbriated enterotoxigenic Escherichia coli (F4-ETEC) in post-weaning piglets. Thirty 31-day-old weaned piglets were randomly allocated to three treatment groups. The positive control (PC) group received colistin via drinking water from d 8 to 14 post-weaning and the same basal diet as the negative control (NC) group; the treatment group received the basal diet with PFA supplementation (1 g/kg of feed). The experiment lasted 21 days. At day 9 post-weaning, all piglets were orally administered 3.0 × 10¹⁰ CFU/piglet of the F4-ETEC strain. The PC piglets had higher fecal consistency than the NC and PFA piglets. PFA supplementation resulted in a lower percentage of piglets excreting F4-ETEC in the feces on days 4–7 post-challenge than in the NC group (p < 0.05) but a higher percentage versus the PC group on day 3–7 post-challenge (p < 0.05). The number of goblet cells (GCs) in the jejunum of the PFA piglets was higher than the NC and PC piglets (p < 0.01). The GC density in the jejunum of the PFA piglets was larger than in the PC piglets (p < 0.05) and similar to the NC piglets (p > 0.10). Mucus thickness in the jejunum of the PFA piglets was similar to the NC piglets and PC piglets (p > 0.10). In conclusion, PFA supplementation to the F4-ETEC-challenged piglets reduced the prevalence of fecal E. coli excretion and improved jejunal histomorphology. Full article

(1) Background: In recent years, the increasing emergence of multidrug-resistant pathogens in pig farms has begun to pose a severe threat to animal welfare and, by extension, public health. In this study, we aimed to explore the biological characteristics and genomic features of bacteriophages that are capable of lysing porcine multidrug-resistant E. coli, which was isolated from sewage. In doing so, we provided a reference for phage therapies that can be used to treat multidrug-resistant strains. (2) Method: Using the multidrug-resistant E. coli isolate sq-1 as the host bacterium, bacteriophages were isolated and purified from fecal samples using a double-layer agar plate method. The morphology was observed using a transmission electron microscope, and its host range, optimal multiplicity of infection (MOI), one-step growth curve, thermal stability, acid–base tolerance, and in vitro antibacterial ability were tested. Genomic features were analyzed using whole-genome sequencing. (3) Results: A lytic phage named vB_EcoS_Psq-1 (abbreviated as Psq-1) was successfully isolated. Electron microscopy revealed that Psq-1 belongs to the family of long-tailed phages, possessing clear and transparent plaques of approximately 1 mm in diameter. Psq-1 only lyses the host bacterium and does not affect other E. coli strains or other species of bacteria. The optimal MOI for phage Psq-1 was 0.1, with a latent period of 25 min, an exponential growth period of 25 min, and a lysis yield of 44.21 PFU/cell. Its activity remains stable at temperatures between 40 °C and 60 °C and from pH 4.0 to pH 13.0. Psq-1 exhibited a significant inhibitory effect on E. coli in liquid culture medium. The nucleic acid type of phage Psq-1 was dsDNA, with a total genome length of 44,183 bp and a GC content of 52.16%. No known resistance, lysogenic, or virulence-related genes were detected. The whole genome contains 55 open reading frames (ORFs). (4) Conclusions: This study isolated a bacteriophage that is capable of lysing multidrug-resistant E. coli. Characterized by a narrow E. coli lysis range, a long latent period, limited lytic ability, and stable biological properties, this bacteriophage can serve as a reference isolate for E. coli phages and can provide biological materials and data to support research on bacteriophages that are effective against multidrug-resistant porcine E. coli. Full article

Background/Objectives: According to the One Health concept, wild birds can be indicators of ecosystem pollution and disease incidence. Escherichia coli strains are widespread worldwide, but there are still few reports on the association of human infections with a potential reservoir of highly pathogenic human strains in wild birds. Fecal E. coli with uropathogenic potential (UPEC) can be transmitted between birds and humans and may be a risk factor for urinary tract infections (UTIs). Results: The results showed that above 50% of the isolates were grouped as highly pathogenic, according to Clermont phylogroup classification. Such strains were found to be stronger biofilm producers, with a higher adherence of monocytes than low pathogenic. However, the highest cytotoxicity was observed for strains described as aquatic environmental. Convergence of the results of the analysis of monocyte activation by E. coli strains and the ability to form biofilm by individual phylogroups of the strains tested was demonstrated. Genetic determinants of the uropathogenicity of E. coli (UPEC) correlate with the evidence of strain pathogenicity during monocyte activation in in vitro assays. Methods: In this study, we assessed the virulence potential of environmental strains isolated from wild waterfowl using genetic analysis (Clermont phylogroup classification) and phenotypic methods, including analysis of the human monocyte response to biofilm formation. The estimation of the ability to form biofilms was tested using crystal violet, and the pathogenic potential of strains by monocyte activation assay including changes in morphology, adhesion and cytotoxicity. Conclusions: In conclusion, the virulence of E. coli strains isolated from free-living birds is significant, and they can be considered environmental reservoirs of pathogenic strains. According to our observations, they can be responsible for the dissemination of uropathogenic strains among humans. Full article

Enteropathogenic (EPEC), necrotoxigenic (NTEC), and Shiga-toxin producing Escherichia coli (STEC) are pathotypes responsible for severe clinical forms in humans and animals. They can be shed in the feces of animals with consequent environmental contamination. This study evaluated the antibacterial activity of essential oils (EOs) from oregano (Origanum vulgare), savory (Satureja montana), thyme (Thymus vulgaris), and their blend against EPEC, NTEC, and STEC strains previously isolated from avian fecal samples. Minimum inhibitory concentration values between 0.039% and 0.156% were found with O. vulgare EO, between ≤0.0195% and 0.156% with both S. montana and T. vulgaris EOs, and between 0.039% and ≤0.0195% with the blend. The mixture with equal parts of EOs from oregano, savory and thyme seems a promising alternative product to combat pathogenic E. coli strains responsible for environmental contamination. Full article